The Environmental Protection Agency is putting the brakes on the massive Pebble Mine project in Alaska, saying it endangers the finest wild salmon run on Earth.

EPA Administrator Gina McCarthy said Friday that her agency would come up with ways to protect the salmon. That process could end with the agency banning the mine before developers even submit plans for review, an extremely unusual step for it to take.

The Army Corps of Engineers won’t be allowed to issue the necessary permit for the mine until the EPA decides what to do.

“Extensive scientific study has given us ample reason to believe that the Pebble Mine would likely have significant and irreversible negative impacts on the Bristol Bay watershed and its abundant salmon fisheries,” McCarthy said. “It’s why EPA is taking this step forward in our effort to ensure protection for the world’s most productive salmon fishery from the risks it faces from what could be one of the largest open pit mines on Earth.”

The EPA released a report last month that said the mine could destroy up to 94 miles of salmon streams and 5,350 acres of wetlands, ponds and lakes. McCarthy visited the region last summer and was clearly moved as Alaska Natives opposed to the project described their cultural ties to the salmon.

The EPA said Friday that it was taking action under the Clean Water Act to protect the salmon, a process that could involve restricting or vetoing the mine.

McCarthy acknowledged that considering a veto of a project before the developers apply for permits is a nearly unprecedented step by the agency. She said this was a unique case, and didn’t reflect a broad change of policy.

White House Press Secretary Jay Carney agreed that Bristol Bay is a unique environment, saying it has an unparalleled sockeye salmon fishery and Native American cultures. Carney said the president strongly supported the EPA’s decision to intervene.

“The step is consistent with the president’s commitment in the State of the Union to protect pristine American places for future generations,” Carney said.

Federal officials said developers would have a chance to make their case before the EPA made a final decision on the mine.

Mine developer Northern Dynasty Minerals said it welcomed the opportunity, saying it planned to blow holes in the arguments the EPA offered.

“We’re kind of eager to get this process started so we can drive a stake in the silly notion of vetoing this project as soon as possible,” said Tom Collier, who leads the company’s efforts on Pebble.

Collier questioned whether the EPA has the legal authority to pre-emptively block the project before it applies for permits. He said the agency had based its scientific assessment on a hypothetical mine rather than on any final plan submitted by Northern Dynasty for regulatory approval.

“If they try to base any decision on the watershed assessment, I think they will have a serious problem,” he said.

The EPA’s decision is the latest in a series of setbacks to the Canadian company’s efforts to develop the giant copper deposit. The British mining giant Anglo American pulled out of the project in September, and the global mining company Rio Tinto, which owns 19 percent of Northern Dynasty, then said it was considering dumping its stake.

Rio Tinto has stayed on, but the pullout of Anglo American leaves Northern Dynasty in need of a new partner to bankroll the work.

Alaska Republican Sen. Lisa Murkowski said Friday that she hadn’t staked out a position on the mine. But Murkowski blasted the EPA’s action, saying that pre-emptively vetoing the mine would set a terrible precedent for projects nationwide.

“If this action is allowed to stand, where will the next ‘unique’ circumstance arise?” Murkowski said in a statement.